data_4DWB
#
_model_server_result.job_id            yMfnk5ahMa9qfJB4DuF6vA 
_model_server_result.datetime_utc      '2024-11-24 06:48:12' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          4dwb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":509}' 
#
_entry.id    4DWB 
#
_exptl.entry_id    4DWB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              275.176 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[2-(pentylamino)ethane-1,1-diyl]bis(phosphonic acid)' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            4DWB 
_cell.length_a            57.871 
_cell.length_b            57.871 
_cell.length_c            392.442 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DWB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+5/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 28.9355 50.117756 327.035 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             J 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OD1 ASP 98 A ASP 98 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc2 A OD2 ASP 98 A ASP 98 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc3 A OD2 ASP 102 A ASP 102 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc4 A OD2 ASP 102 A ASP 102 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc5 A O ILE 129 A ILE 129 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc6 A OD2 ASP 250 A ASP 250 1_555 I MG MG . A MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc7 F NA NA . A NA 505 1_555 K O HOH . A HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.084 ? 
metalc ? metalc8 G MG MG . A MG 506 1_555 J O14 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc9 G MG MG . A MG 506 1_555 K O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc10 G MG MG . A MG 506 1_555 K O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? 
metalc ? metalc11 G MG MG . A MG 506 1_555 K O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc12 H MG MG . A MG 507 1_555 J O14 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? 
metalc ? metalc13 H MG MG . A MG 507 1_555 J O13 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc14 H MG MG . A MG 507 1_555 K O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc15 H MG MG . A MG 507 1_555 K O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc16 I MG MG . A MG 508 1_555 J O15 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? 
metalc ? metalc17 I MG MG . A MG 508 1_555 J O11 0M7 . A 0M7 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc18 I MG MG . A MG 508 1_555 K O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc19 I MG MG . A MG 508 1_555 K O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc20 I MG MG . A MG 508 1_555 K O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
#
_chem_comp.formula           'C7 H19 N O6 P2' 
_chem_comp.formula_weight    275.176 
_chem_comp.id                0M7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[2-(pentylamino)ethane-1,1-diyl]bis(phosphonic acid)' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C10 C9 0M7 sing 1 n n 
C8 C9 0M7 sing 2 n n 
C8 C7 0M7 sing 3 n n 
C7 C6 0M7 sing 4 n n 
C6 N5 0M7 sing 5 n n 
O13 P3 0M7 doub 6 n n 
O12 P3 0M7 sing 7 n n 
C4 N5 0M7 sing 8 n n 
C4 C2 0M7 sing 9 n n 
P3 C2 0M7 sing 10 n n 
P3 O11 0M7 sing 11 n n 
O14 P1 0M7 doub 12 n n 
C2 P1 0M7 sing 13 n n 
P1 O16 0M7 sing 14 n n 
P1 O15 0M7 sing 15 n n 
O11 H1 0M7 sing 16 n n 
O12 H2 0M7 sing 17 n n 
C2 H3 0M7 sing 18 n n 
O15 H4 0M7 sing 19 n n 
O16 H5 0M7 sing 20 n n 
C4 H6 0M7 sing 21 n n 
C4 H7 0M7 sing 22 n n 
N5 H8 0M7 sing 23 n n 
C6 H10 0M7 sing 24 n n 
C6 H11 0M7 sing 25 n n 
C7 H12 0M7 sing 26 n n 
C7 H13 0M7 sing 27 n n 
C8 H14 0M7 sing 28 n n 
C8 H15 0M7 sing 29 n n 
C9 H16 0M7 sing 30 n n 
C9 H17 0M7 sing 31 n n 
C10 H18 0M7 sing 32 n n 
C10 H19 0M7 sing 33 n n 
C10 H20 0M7 sing 34 n n 
#
_atom_sites.entry_id                     4DWB 
_atom_sites.fract_transf_matrix[1][1]    0.01728 
_atom_sites.fract_transf_matrix[1][2]    0.009977 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019953 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.002548 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 IPE A 1 501 501 IPE IPR . 
C 3 SO4 A 1 502 1 SO4 SO4 . 
D 3 SO4 A 1 503 2 SO4 SO4 . 
E 4 ACT A 1 504 3 ACT ACT . 
F 5 NA A 1 505 4 NA NA . 
G 6 MG A 1 506 401 MG MG . 
H 6 MG A 1 507 402 MG MG . 
I 6 MG A 1 508 403 MG MG . 
J 7 0M7 A 1 509 500 0M7 BR6 . 
K 8 HOH A 1 601 1 HOH HOH . 
K 8 HOH A 2 602 2 HOH HOH . 
K 8 HOH A 3 603 3 HOH HOH . 
K 8 HOH A 4 604 4 HOH HOH . 
K 8 HOH A 5 605 5 HOH HOH . 
K 8 HOH A 6 606 6 HOH HOH . 
K 8 HOH A 7 607 7 HOH HOH . 
K 8 HOH A 8 608 11 HOH HOH . 
K 8 HOH A 9 609 12 HOH HOH . 
K 8 HOH A 10 610 13 HOH HOH . 
K 8 HOH A 11 611 14 HOH HOH . 
K 8 HOH A 12 612 15 HOH HOH . 
K 8 HOH A 13 613 16 HOH HOH . 
K 8 HOH A 14 614 17 HOH HOH . 
K 8 HOH A 15 615 18 HOH HOH . 
K 8 HOH A 16 616 19 HOH HOH . 
K 8 HOH A 17 617 21 HOH HOH . 
K 8 HOH A 18 618 23 HOH HOH . 
K 8 HOH A 19 619 24 HOH HOH . 
K 8 HOH A 20 620 25 HOH HOH . 
K 8 HOH A 21 621 26 HOH HOH . 
K 8 HOH A 22 622 27 HOH HOH . 
K 8 HOH A 23 623 28 HOH HOH . 
K 8 HOH A 24 624 30 HOH HOH . 
K 8 HOH A 25 625 32 HOH HOH . 
K 8 HOH A 26 626 33 HOH HOH . 
K 8 HOH A 27 627 34 HOH HOH . 
K 8 HOH A 28 628 35 HOH HOH . 
K 8 HOH A 29 629 36 HOH HOH . 
K 8 HOH A 30 630 37 HOH HOH . 
K 8 HOH A 31 631 38 HOH HOH . 
K 8 HOH A 32 632 39 HOH HOH . 
K 8 HOH A 33 633 40 HOH HOH . 
K 8 HOH A 34 634 41 HOH HOH . 
K 8 HOH A 35 635 43 HOH HOH . 
K 8 HOH A 36 636 44 HOH HOH . 
K 8 HOH A 37 637 45 HOH HOH . 
K 8 HOH A 38 638 46 HOH HOH . 
K 8 HOH A 39 639 47 HOH HOH . 
K 8 HOH A 40 640 48 HOH HOH . 
K 8 HOH A 41 641 49 HOH HOH . 
K 8 HOH A 42 642 51 HOH HOH . 
K 8 HOH A 43 643 52 HOH HOH . 
K 8 HOH A 44 644 53 HOH HOH . 
K 8 HOH A 45 645 54 HOH HOH . 
K 8 HOH A 46 646 55 HOH HOH . 
K 8 HOH A 47 647 56 HOH HOH . 
K 8 HOH A 48 648 57 HOH HOH . 
K 8 HOH A 49 649 58 HOH HOH . 
K 8 HOH A 50 650 60 HOH HOH . 
K 8 HOH A 51 651 61 HOH HOH . 
K 8 HOH A 52 652 62 HOH HOH . 
K 8 HOH A 53 653 64 HOH HOH . 
K 8 HOH A 54 654 65 HOH HOH . 
K 8 HOH A 55 655 66 HOH HOH . 
K 8 HOH A 56 656 67 HOH HOH . 
K 8 HOH A 57 657 68 HOH HOH . 
K 8 HOH A 58 658 69 HOH HOH . 
K 8 HOH A 59 659 70 HOH HOH . 
K 8 HOH A 60 660 71 HOH HOH . 
K 8 HOH A 61 661 72 HOH HOH . 
K 8 HOH A 62 662 73 HOH HOH . 
K 8 HOH A 63 663 74 HOH HOH . 
K 8 HOH A 64 664 75 HOH HOH . 
K 8 HOH A 65 665 76 HOH HOH . 
K 8 HOH A 66 666 77 HOH HOH . 
K 8 HOH A 67 667 79 HOH HOH . 
K 8 HOH A 68 668 80 HOH HOH . 
K 8 HOH A 69 669 82 HOH HOH . 
K 8 HOH A 70 670 83 HOH HOH . 
K 8 HOH A 71 671 84 HOH HOH . 
K 8 HOH A 72 672 85 HOH HOH . 
K 8 HOH A 73 673 86 HOH HOH . 
K 8 HOH A 74 674 87 HOH HOH . 
K 8 HOH A 75 675 88 HOH HOH . 
K 8 HOH A 76 676 89 HOH HOH . 
K 8 HOH A 77 677 90 HOH HOH . 
K 8 HOH A 78 678 91 HOH HOH . 
K 8 HOH A 79 679 92 HOH HOH . 
K 8 HOH A 80 680 93 HOH HOH . 
K 8 HOH A 81 681 94 HOH HOH . 
K 8 HOH A 82 682 95 HOH HOH . 
K 8 HOH A 83 683 96 HOH HOH . 
K 8 HOH A 84 684 97 HOH HOH . 
K 8 HOH A 85 685 98 HOH HOH . 
K 8 HOH A 86 686 99 HOH HOH . 
K 8 HOH A 87 687 100 HOH HOH . 
K 8 HOH A 88 688 101 HOH HOH . 
K 8 HOH A 89 689 102 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O11 0M7 . . . J 7 13.15 13.248 177.641 1 33.27 ? O11 0M7 509 A 1 
HETATM 2 P P3 0M7 . . . J 7 12.8 14.094 176.456 1 29.91 ? P3 0M7 509 A 1 
HETATM 3 O O13 0M7 . . . J 7 13.969 14.315 175.487 1 30.63 ? O13 0M7 509 A 1 
HETATM 4 O O12 0M7 . . . J 7 11.52 13.649 175.806 1 34.73 ? O12 0M7 509 A 1 
HETATM 5 C C2 0M7 . . . J 7 12.327 15.718 177.085 1 34.15 ? C2 0M7 509 A 1 
HETATM 6 P P1 0M7 . . . J 7 13.666 16.556 177.99 1 33.63 ? P1 0M7 509 A 1 
HETATM 7 O O15 0M7 . . . J 7 14.021 15.55 179.058 1 31.35 ? O15 0M7 509 A 1 
HETATM 8 O O14 0M7 . . . J 7 14.709 16.762 176.902 1 35.93 ? O14 0M7 509 A 1 
HETATM 9 O O16 0M7 . . . J 7 13.13 17.849 178.486 1 35.3 ? O16 0M7 509 A 1 
HETATM 10 C C4 0M7 . . . J 7 11.967 16.508 175.839 1 35.8 ? C4 0M7 509 A 1 
HETATM 11 N N5 0M7 . . . J 7 10.757 17.252 176.16 1 40.99 ? N5 0M7 509 A 1 
HETATM 12 C C6 0M7 . . . J 7 10.287 18.264 175.24 1 38.24 ? C6 0M7 509 A 1 
HETATM 13 C C7 0M7 . . . J 7 11.319 19.385 175.132 1 39.01 ? C7 0M7 509 A 1 
HETATM 14 C C8 0M7 . . . J 7 11.251 20.04 173.765 1 39.4 ? C8 0M7 509 A 1 
HETATM 15 C C9 0M7 . . . J 7 10.408 21.284 173.849 1 40.79 ? C9 0M7 509 A 1 
HETATM 16 C C10 0M7 . . . J 7 8.997 20.952 173.372 1 40.31 ? C10 0M7 509 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#